src/nf_modules/Bowtie/tests.sh

-./nextflow src/nf_modules/Bowtie/indexing.nf \
-  -c src/nf_modules/Bowtie/indexing.config \
-  -profile docker \
-  --fasta "data/tiny_dataset/fasta/tiny_v2.fasta"
-
-./nextflow src/nf_modules/Bowtie/mapping_single.nf \
-  -c src/nf_modules/Bowtie/mapping_single.config \
-  -profile docker \
-  --index "results/mapping/index/*.ebwt" \
-  --fastq "data/tiny_dataset/fastq/tiny*_S.fastq"
-
-./nextflow src/nf_modules/Bowtie/mapping_paired.nf \
-  -c src/nf_modules/Bowtie/mapping_paired.config \
-  -profile docker \
-  --index "results/mapping/index/*.ebwt" \
-  --fastq "data/tiny_dataset/fastq/tiny*_R{1,2}.fastq"
-

src/nf_modules/Bowtie2/indexing.config

-profiles {
-  docker {
-    docker.temp = 'auto'
-    docker.enabled = true
-    process {
-      $index_fasta {
-        container = "bowtie2:2.3.4.1"
-      }
-    }
-  }
-  sge {
-    process{
-      $index_fasta {
-        beforeScript = "module purge; module load Bowtie2/2.3.4.1"
-      }
-    }
-  }
-}

src/nf_modules/Bowtie2/indexing.nf

-params.fasta = "$baseDir/data/bam/*.fasta"
-
-log.info "fasta files : ${params.fasta}"
-
-Channel
-  .fromPath( params.fasta )
-  .ifEmpty { error "Cannot find any bam files matching: ${params.fasta}" }
-  .set { fasta_file }
-
-process index_fasta {
-  tag "$fasta.baseName"
-  cpus 4
-  publishDir "results/mapping/index/", mode: 'copy'
-
-  input:
-    file fasta from fasta_file
-
-  output:
-    file "*.index*" into index_files
-    file "*_report.txt" into indexing_report
-
-  script:
-"""
-bowtie2-build --threads ${task.cpus} ${fasta} ${fasta.baseName}.index &> ${fasta.baseName}_bowtie2_report.txt
-
-if grep -q "Error" ${fasta.baseName}_bowtie2_report.txt; then
-  exit 1
-fi
-"""
-}
-
-

src/nf_modules/Bowtie2/mapping_paired.config

-profiles {
-  docker {
-    docker.temp = 'auto'
-    docker.enabled = true
-    process {
-      $mapping_fastq {
-        container = "bowtie2:2.3.4.1"
-      }
-    }
-  }
-  sge {
-    process{
-      $mapping_fastq {
-        beforeScript = "module purge; module load SAMtools/1.7; module load Bowtie2/2.3.4.1"
-      }
-    }
-  }
-}

src/nf_modules/Bowtie2/mapping_paired.nf

-params.fastq = "$baseDir/data/fastq/*_{1,2}.fastq"
-params.index = "$baseDir/data/index/*.index.*"
-
-log.info "fastq files : ${params.fastq}"
-log.info "index files : ${params.index}"
-
-Channel
-  .fromFilePairs( params.fastq )
-  .ifEmpty { error "Cannot find any fastq files matching: ${params.fastq}" }
-  .set { fastq_files }
-Channel
-  .fromPath( params.index )
-  .ifEmpty { error "Cannot find any index files matching: ${params.index}" }
-  .set { index_files }
-
-process mapping_fastq {
-  tag "$pair_id"
-  cpus 4
-  publishDir "results/mapping/bams/", mode: 'copy'
-
-  input:
-  set pair_id, file(reads) from fastq_files
-  file index from index_files.collect()
-
-  output:
-  set pair_id, "*.bam" into bam_files
-  file "*_report.txt" into mapping_report
-
-  script:
-  index_id = index[0]
-  for (index_file in index) {
-    if (index_file =~ /.*\.1\.bt2/ && !(index_file =~ /.*\.rev\.1\.bt2/)) {
-        index_id = ( index_file =~ /(.*)\.1\.bt2/)[0][1]
-    }
-  }
-"""
-bowtie2 --very-sensitive -p ${task.cpus} -x ${index_id} \
--1 ${reads[0]} -2 ${reads[1]} 2> \
-${pair_id}_bowtie2_report.txt | \
-samtools view -Sb - > ${pair_id}.bam
-
-if grep -q "Error" ${pair_id}_bowtie2_report.txt; then
-  exit 1
-fi
-"""
-}
-

src/nf_modules/Bowtie2/mapping_single.config

-profiles {
-  docker {
-    docker.temp = 'auto'
-    docker.enabled = true
-    process {
-      $mapping_fastq {
-        container = "bowtie2:2.3.4.1"
-      }
-    }
-  }
-  sge {
-    process{
-      $mapping_fastq {
-        beforeScript = "module purge; module load SAMtools/1.7; module load Bowtie2/2.3.4.1"
-      }
-    }
-  }
-}

src/nf_modules/Bowtie2/mapping_single.nf

-params.fastq = "$baseDir/data/fastq/*.fastq"
-
-log.info "fastq files : ${params.fastq}"
-log.info "index files : ${params.index}"
-
-Channel
-  .fromPath( params.fastq )
-  .ifEmpty { error "Cannot find any fastq files matching: ${params.fastq}" }
-  .map { it -> [(it.baseName =~ /([^\.]*)/)[0][1], it]}
-  .set { fastq_files }
-Channel
-  .fromPath( params.index )
-  .ifEmpty { error "Cannot find any index files matching: ${params.index}" }
-  .set { index_files }
-
-process mapping_fastq {
-  tag "$file_id"
-  cpus 4
-  publishDir "results/mapping/bams/", mode: 'copy'
-
-  input:
-  set file_id, file(reads) from fastq_files
-  file index from index_files.collect()
-
-  output:
-  set file_id, "*.bam" into bam_files
-  file "*_report.txt" into mapping_report
-
-  script:
-  index_id = index[0]
-  for (index_file in index) {
-    if (index_file =~ /.*\.1\.bt2/ && !(index_file =~ /.*\.rev\.1\.bt2/)) {
-        index_id = ( index_file =~ /(.*)\.1\.bt2/)[0][1]
-    }
-  }
-"""
-bowtie2 --very-sensitive -p ${task.cpus} -x ${index_id} \
--U ${reads} 2> \
-${file_id}_bowtie2_report.txt | \
-samtools view -Sb - > ${file_id}.bam
-
-if grep -q "Error" ${file_id}_bowtie2_report.txt; then
-  exit 1
-fi
-"""
-}

src/nf_modules/Bowtie2/tests.sh

-./nextflow src/nf_modules/Bowtie2/indexing.nf \
-  -c src/nf_modules/Bowtie2/indexing.config \
-  -profile docker \
-  --fasta "data/tiny_dataset/fasta/tiny_v2.fasta"
-
-./nextflow src/nf_modules/Bowtie2/mapping_single.nf \
-  -c src/nf_modules/Bowtie2/mapping_single.config \
-  -profile docker \
-  --index "data/tiny_dataset/fasta/*.bt2" \
-  --fastq "data/tiny_dataset/fastq/tiny*_S.fastq"
-
-./nextflow src/nf_modules/Bowtie2/mapping_paired.nf \
-  -c src/nf_modules/Bowtie2/mapping_paired.config \
-  -profile docker \
-  --index "data/tiny_dataset/fasta/*.bt2" \
-  --fastq "data/tiny_dataset/fastq/tiny*_R{1,2}.fastq"
-

src/nf_modules/FastQC/fastqc_paired.config

-profiles {
-  docker {
-    docker.temp = 'auto'
-    docker.enabled = true
-    process {
-      $fastqc_fastq {
-        container = "fastqc:0.11.5"
-      }
-    }
-  }
-  sge {
-    process{
-      $fastqc_fastq {
-        beforeScript = "module purge; module load FastQC/0.11.5"
-        executor = "sge"
-        cpus = 1
-        memory = "5GB"
-        time = "6h"
-        queueSize = 1000
-        pollInterval = '60sec'
-        queue = 'monointeldeb128'
-      }
-    }
-  }
-}

src/nf_modules/FastQC/fastqc_paired.nf

-params.fastq = "$baseDir/data/fastq/*_{1,2}.fastq"
-
-log.info "fastq files : ${params.fastq}"
-
-Channel
-  .fromFilePairs( params.fastq )
-  .ifEmpty { error "Cannot find any fastq files matching: ${params.fastq}" }
-  .set { fastq_files }
-
-process fastqc_fastq {
-  tag "$pair_id"
-  publishDir "results/fastq/fastqc/", mode: 'copy'
-
-  input:
-  set pair_id, file(reads) from fastq_files
-
-  output:
-    file "*.{zip,html}" into fastqc_report
-
-  script:
-"""
-fastqc --quiet --threads ${task.cpus} --format fastq --outdir ./ \
-${reads[0]} ${reads[1]}
-"""
-}
-

src/nf_modules/FastQC/fastqc_single.config

-profiles {
-  docker {
-    docker.temp = 'auto'
-    docker.enabled = true
-    process {
-      $fastqc_fastq {
-        container = "fastqc:0.11.5"
-      }
-    }
-  }
-  sge {
-    process{
-      $fastqc_fastq {
-        beforeScript = "module purge; module load FastQC/0.11.5"
-        executor = "sge"
-        cpus = 1
-        memory = "5GB"
-        time = "6h"
-        queueSize = 1000
-        pollInterval = '60sec'
-        queue = 'monointeldeb128'
-      }
-    }
-  }
-}

src/nf_modules/FastQC/fastqc_single.nf

-params.fastq = "$baseDir/data/fastq/*.fastq"
-
-log.info "fastq files : ${params.fastq}"
-
-Channel
-  .fromPath( params.fastq )
-  .ifEmpty { error "Cannot find any fastq files matching: ${params.fastq}" }
-  .map { it -> [(it.baseName =~ /([^\.]*)/)[0][1], it]}
-  .set { fastq_files }
-
-process fastqc_fastq {
-  tag "$file_id"
-  publishDir "results/fastq/fastqc/", mode: 'copy'
-  cpus = 1
-
-  input:
-  set file_id, file(reads) from fastq_files
-
-  output:
-    file "*.{zip,html}" into fastqc_report
-
-  script:
-"""
-fastqc --quiet --threads ${task.cpus} --format fastq --outdir ./ ${reads}
-"""
-}
-

src/nf_modules/FastQC/tests.sh

-./nextflow src/nf_modules/FastQC/fastqc_paired.nf \
-  -c src/nf_modules/FastQC/fastqc_paired.config \
-  -profile docker \
-  --fastq "data/tiny_dataset/fastq/tiny_R{1,2}.fastq"
-
-./nextflow src/nf_modules/FastQC/fastqc_single.nf \
-  -c src/nf_modules/FastQC/fastqc_single.config \
-  -profile docker \
-  --fastq "data/tiny_dataset/fastq/tiny_S.fastq"

src/nf_modules/HTSeq/htseq.config

-profiles {
-  docker {
-    docker.temp = 'auto'
-    docker.enabled = true
-    process {
-      $sort_bam {
-        container = "samtools:1.7"
-      }
-      $counting {
-        container = "htseq:0.8.0"
-      }
-    }
-  }
-  sge {
-    process{
-      $sort_bam {
-        beforeScript = "module purge; module load SAMtools/1.7"
-      }
-      $trimming {
-        beforeScript = "module purge; module load HTSeq/0.8.0"
-      }
-    }
-  }
-}

src/nf_modules/HTSeq/htseq.nf

-params.bam = "$baseDir/data/bam/*.bam"
-params.gtf = "$baseDir/data/annotation/*.gtf"
-
-log.info "bam files : ${params.bam}"
-log.info "gtf files : ${params.gtf}"
-
-Channel
-  .fromPath( params.bam )
-  .ifEmpty { error "Cannot find any fastq files matching: ${params.bam}" }
-  .map { it -> [(it.baseName =~ /([^\.]*)/)[0][1], it]}
-  .set { bam_files }
-Channel
-  .fromPath( params.gtf )
-  .ifEmpty { error "Cannot find any gtf file matching: ${params.gtf}" }
-  .set { gtf_file }
-
-process sort_bam {
-  tag "$file_id"
-  cpus 4
-
-  input:
-    set file_id, file(bam) from bam_files
-
-  output:
-    set file_id, "*_sorted.sam" into sorted_bam_files
-
-  script:
-"""
-# sort bam by name
-samtools sort -@ ${task.cpus} -n -O SAM -o ${file_id}_sorted.sam ${bam}
-"""
-}
-
-process counting {
-  tag "$file_id"
-  publishDir "results/quantification/", mode: 'copy'
-
-  input:
-  set file_id, file(bam) from sorted_bam_files
-  file gtf from gtf_file
-
-  output:
-  file "*.count" into count_files
-
-  script:
-"""
-htseq-count ${bam} ${gtf} \
--r pos --mode=intersection-nonempty -a 10 -s no -t exon -i gene_id \
-> ${file_id}.count
-"""
-}
-

src/nf_modules/HTSeq/tests.sh

-./nextflow src/nf_modules/HTSeq/htseq.nf \
-  -c src/nf_modules/HTSeq/htseq.config \
-  -profile docker \
-  --gtf "data/tiny_dataset/annot/tiny.gff" \
-  --bam "data/tiny_dataset/map/tiny_v2.bam"
-

src/nf_modules/Kallisto/indexing.config

-profiles {
-  docker {
-    docker.temp = 'auto'
-    docker.enabled = true
-    process {
-      $index_fasta {
-        container = "kallisto:0.44.0"
-      }
-    }
-  }
-  sge {
-    process{
-      $index_fasta {
-        beforeScript = "module purge; module load Kallisto/0.44.0"
-        executor = "sge"
-        cpus = 1
-        memory = "5GB"
-        time = "6h"
-        queueSize = 1000
-        pollInterval = '60sec'
-        queue = 'h6-E5-2667v4deb128'
-        penv = 'openmp8'
-      }
-    }
-  }
-}

src/nf_modules/Kallisto/indexing.nf

-params.fasta = "$baseDir/data/bam/*.fasta"
-
-log.info "fasta files : ${params.fasta}"
-
-Channel
-  .fromPath( params.fasta )
-  .ifEmpty { error "Cannot find any bam files matching: ${params.fasta}" }
-  .set { fasta_file }
-
-process index_fasta {
-  tag "$fasta.baseName"
-  cpus 4
-  publishDir "results/mapping/index/", mode: 'copy'
-
-  input:
-    file fasta from fasta_file
-
-  output:
-    file "*.index*" into index_files
-    file "*_kallisto_report.txt" into index_files_report
-
-  script:
-"""
-kallisto index -k 31 --make-unique -i ${fasta.baseName}.index ${fasta} \
-2> ${fasta.baseName}_kallisto_report.txt
-"""
-}
-

src/nf_modules/Kallisto/mapping_paired.config

-profiles {
-  docker {
-    docker.temp = 'auto'
-    docker.enabled = true
-    process {
-      $mapping_fastq {
-        container = "kallisto:0.44.0"
-      }
-    }
-  }
-  sge {
-    process{
-      $mapping_fastq {
-        beforeScript = "module purge; module load Kallisto/0.44.0"
-        executor = "sge"
-        cpus = 4
-        memory = "5GB"
-        time = "6h"
-        queueSize = 1000
-        pollInterval = '60sec'
-        queue = 'h6-E5-2667v4deb128'
-        penv = 'openmp8'
-      }
-    }
-  }
-}

src/nf_modules/Kallisto/mapping_paired.nf

-params.fastq = "$baseDir/data/fastq/*_{1,2}.fastq"
-params.index = "$baseDir/data/index/*.index.*"
-
-log.info "fastq files : ${params.fastq}"
-log.info "index files : ${params.index}"
-
-Channel
-  .fromFilePairs( params.fastq )
-  .ifEmpty { error "Cannot find any fastq files matching: ${params.fastq}" }
-  .set { fastq_files }
-Channel
-  .fromPath( params.index )
-  .ifEmpty { error "Cannot find any index files matching: ${params.index}" }
-  .set { index_files }
-
-process mapping_fastq {
-  tag "$reads"
-  cpus 4
-  publishDir "results/mapping/quantification/", mode: 'copy'
-
-  input:
-  set pair_id, file(reads) from fastq_files
-  file index from index_files.collect()
-
-  output:
-  file "*" into counts_files
-
-  script:
-"""
-mkdir ${pair_id}
-kallisto quant -i ${index} -t ${task.cpus} \
---bias --bootstrap-samples 100 -o ${pair_id} \
-${reads[0]} ${reads[1]} &> ${pair_id}/kallisto_report.txt
-"""
-}
-